def write(data, file):
file_existed = True if exists(file) else False
io.write_file(
data,
io.absolute_path(file, __dirname),
)
return file_existed
def main():
def add_arguments(parser):
parser.add_argument('-d', '--delim', default="\t")
parser.add_argument('infile', type='readable_file')
parser.add_argument('termfile', type='readable_file')
parser.add_argument('outfile', type='writeable_file', nargs='?', default=None)
ns = parse(add_arguments)
with open(ns.infile, 'rU') as f:
s = f.read()
for find, repl in csv_to_table(ns.termfile, ns.delim):
s = re.sub(find, repl, s)
outfile = ns.outfile or ns.infile
write_file(outfile, s)
def main():
def add_arguments(parser):
parser.add_argument('-d', '--delim', default="\t")
parser.add_argument('infile', type='readable_file')
parser.add_argument('termfile', type='readable_file')
parser.add_argument('outfile',
type='writeable_file',
nargs='?',
default=None)
ns = parse(add_arguments)
with open(ns.infile, 'rU') as f:
s = f.read()
for find, repl in csv_to_table(ns.termfile, ns.delim):
s = re.sub(find, repl, s)
outfile = ns.outfile or ns.infile
write_file(outfile, s)
def translate(**kwargs):
# Another way to do this is like:
# source = 'en'
# try:
# source = kwargs['source']
# except KeyError:
# pass
source = "en" if "source" not in kwargs else kwargs["source"]
dest = "es" if "dest" not in kwargs else kwargs["dest"]
file = None if "file" not in kwargs else kwargs["file"]
text = None if "text" not in kwargs else kwargs["text"]
if not text and not file:
source = input("Enter the source language: ")
dest = input("Enter the destination language: ")
text = input("Enter a text to translate: ")
elif file:
if isinstance(file, str) and not Path(file).is_file():
raise TranslateException("Please provide a valid path to a file")
if isinstance(file, str) and Path(file).suffix != ".txt":
raise TranslateException("Only .txt files are allowed")
text = read_file(file)
translated_text = ""
try:
translated_text = Translator().translate(text,
dest=dest,
source=source).text
except ValueError as verror:
raise TranslateException(
"The source or destination language is invalid.") from verror
except Exception as ex:
raise ApiException(
"An error ocurred while connecting with the API") from ex
else:
if file:
output_file = ("data/output.txt"
if "output" not in kwargs else kwargs["output"])
write_file(translated_text, output_file)
return translated_text
#Revertendo a String
alignedseq1 = alignedseq1[::-1]
alignedseq2 = alignedseq2[::-1]
return alignedseq1, alignedseq2
if __name__ == '__main__':
#Definicoes dos parametros
par = Parameters(gapopen=-10, gap=-0.5, matrix='BLOSUM62', stype='protein')
#Sequencias
seq1 = io.read_fasta(io.read_file("../inputs/default1.fasta"))
seq2 = io.read_fasta(io.read_file("../inputs/default2.fasta"))
#Matriz de apontadores
M, Ix, Iy = global_align(seq1, seq2, par)
#Sequencias alinhadas
leftalignedseq1, leftalignedseq2 = traceback_left(M, Ix, Iy, seq1, seq2,
par)
upalignedseq1, upalignedseq2 = traceback_up(M, Ix, Iy, seq1, seq2, par)
result = Alignment(leftalignedseq1, leftalignedseq2, "LEFT")
result.calculate_mat_mis_gaps()
io.write_file("../outputs/locally_global_affine_output.txt", str(result))
result = Alignment(upalignedseq1, upalignedseq2, "UP")
result.calculate_mat_mis_gaps()
io.append_file("../outputs/locally_global_affine_output.txt", str(result))
def set_state(data):
return io.write_file(
data,
io.absolute_path('state', __dirname, True),
)
if M[i][j] == M[i][j - 1] + Parameters.gap:
#if M[i][j-1] is not 0:
alignedseq1 = alignedseq1 + '-'
alignedseq2 = alignedseq2 + seq2[j - 1]
j = j - 1
continue
#Revertendo a String
alignedseq1 = alignedseq1[::-1]
alignedseq2 = alignedseq2[::-1]
return alignedseq1, alignedseq2
if __name__ == '__main__':
#Definicoes dos parametros
par = Parameters(gap=-10, matrix='BLOSUM62', stype='dna')
seq1 = io.read_fasta(io.read_file("../inputs/default1.fasta"))
seq2 = io.read_fasta(io.read_file("../inputs/default2.fasta"))
matrix, i, j = local_align(seq1, seq2, par)
alignedseq1, alignedseq2 = traceback(matrix, seq1, seq2, i, j, par)
result = Alignment(alignedseq1, alignedseq2, "DEFAULT")
result.calculate_mat_mis_gaps()
io.write_file("../outputs/locally_local_linear_output.txt", str(result))
LOG.info("----------\n")
# RUN
LOG.info("[{0}] Requesting the URL = {1}...".format(datetime.now(),EBI_RUN_URL))
r = requests.post(EBI_RUN_URL,data)
LOG.info("[{0}] Request made and the code returned was {1}".format(datetime.now(),r.status_code))
LOG.info("Nome do job gerado = {}".format(r.text))
#RESULT
LOG.info("[{0}] Requesting the URL = {1}...".format(datetime.now(),EBI_RESULT_URL))
#Addind the jobid
result = requests.get(EBI_RESULT_URL+"{jobID}/aln".format(jobID=r.text))
#Trying again until 200 is returned
while (result.status_code is not 200):
LOG.info("[{0}] Result not ready yet...".format(datetime.now()))
LOG.info("[{0}] Requesting the URL = {1}...".format(datetime.now(),EBI_RESULT_URL))
result = requests.get(EBI_RESULT_URL+"{jobID}/aln".format(jobID=r.text))
LOG.info("[{0}] Results got = {1}...".format(datetime.now(),result.text))
alignment = get_alignment(result.text)
io.write_file("../outputs/ebi_local_output.txt",str(alignment))
#print(str(alignment))
